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Posts about scientific research and development as well as science and engineering breakthroughs.
Recommended posts: R&D Spending in USA Universities - Diplomacy and Science Research - Research Career in Industry or Academia - New Understanding of Human DNA - Basic Science Research Funding - The Worlds Best Research Universities - Mystery of High-Temperature Superconductivity - Why Most Published Research Findings Are False

Chimpanzees Use Spears to Hunt Bush Babies

Savanna Chimpanzees, Pan troglodytes verus, Hunt with Tools by Jill D. Pruetz and Paco Bertolani

Although tool use is known to occur in species ranging from naked mole rats to owls, chimpanzees are the most accomplished tool users. The modification and use of tools during hunting, however, is still considered to be a uniquely human trait among primates. Here, we report the first account of habitual tool use during vertebrate hunting by nonhumans. At the Fongoli site in Senegal, we observed ten different chimpanzees use tools to hunt prosimian prey in 22 bouts. This includes immature chimpanzees and females, members of age-sex classes not normally characterized by extensive hunting behavior. Chimpanzees made 26 different tools, and we were able to recover and analyze 12 of these.

Tool construction entailed up to five steps, including trimming the tool tip to a point. Tools were used in the manner of a spear, rather than a probe or rousing tool. This new information on chimpanzee tool use has important implications for the evolution of tool use and construction for hunting in the earliest hominids, especially given our observations that females and immature chimpanzees exhibited this behavior more frequently than adult males.

The full paper, from 2007, was available as a pdf when I visited (I don’t really trust these publishers and what articles by professors they will block access to later when they don’t clearly say it is open access – in fact the journal broke the link on the post I made about this in 2007 now that I checked – sigh).

The full paper isn’t filled with overly complex scientific jargon (as scientific papers can be). In that sense it is an easy read; it is a bit graphic for those that are squeamish.

Dr. Jill Pruetz maintains an interesting blog the Chimpanzees she studies: Fongoli Savanna Chimpanzee Project

Related: Chimps Used Stones as HammersOrangutan Attempts to Hunt Fish with SpearBird Using Bread as Bait to Catch FishCrows can Perform as Well as 7 to 10-year-olds on cause-and-effect Water Displacement Tasks

Scientific Inquiry Leads to Using Fluoride for Healthy Teeth

This webcast, from the wonderful SciShow, explores how we discovered fluoride helps prevent tooth decay and how we then used that knowledge and finally discovered why it worked.

I love stories of how we learn for observing what is happening. We don’t always need to innovate by thinking up creative new ideas. If we are observant we can pick up anomalies and then examine the situation to find possible explanations and then experiment to see if those explanations prove true.

When working this way we often are seeing correlation and then trying to figure out which part of the correlation is an actual cause. So in this dental example, a dentist noticed his patients had bad brown stains on their teeth than others populations did.

After investigation the natural fluoridation of the water in Colorado Springs, Colorado, USA seemed like it might be an explanation (though they didn’t understand the chemistry that would cause that result). They also explored the sense that the discolored teeth were resistant to decay.

Even without knowing why it is possible to test if the conditions are the cause. Scientists discovered by reducing the level of fluoridation in the water the ugly brown stains could be eliminated (these stains took a long time to develop and didn’t develop in adults). Eventually scientists ran an experiment in Grand Rapids, Michigan and found fluoridation of the water achieved amazing results for dental health. The practice of fluoridation was then adopted widely and resulted in greatly improved dental health.

In 1901, Frederick McKay, a recent dental school graduate, opened a dental practice in Colorado Springs, Colorado. He was interested in what he saw and sought out other dentists to explore the situation with him but had little success. In 1909, he found some success when renowned dental researcher Dr. G.V. Black collaborate with him.
Dr. H. Trendley Dean, head of the Dental Hygiene Unit at the National Institute of Health built on their work when he began investigating the epidemiology of fluorosis in 1931. It wasn’t until 1945 that the Grand Rapids test started. Science can take a long time to move forward.

Only later did scientists unravel why this worked. The fluoride reacts to create a stronger enamel than if the fluoride is not present. Which results in the enamal being less easily dissolved by bacteria.
Health tip: use a dental stimudent (dental picks) or floss your teeth to maintain healthy gums and prevent tooth decay. It makes a big difference.

Related: Why does orange juice taste so bad after brushing your teeth?Microbiologist Develops Mouthwash That Targets Only Harmful Cavity Causing BacteriaUsing Nanocomposites to Improve Dental Filling PerformanceFinding a Dentist in Chiang Mai, ThailandFalse Teeth For CatsWhy Does Hair Turn Grey as We Age?

We Have Thousands of Viruses In Us All the Time

Biology and the amazing interactions within a human body are amazing. Our bodies are teeming with other life (and almost life – viruses). All these microbes have a drastic impact on our health and those impacts are not always bad.

A Virus In Your Mouth Helps Fight The Flu

Hidden inside all of us are likely thousands of viruses — maybe more. They just hang out, harmlessly. We don’t even know they’re there.

But every once in a while, one of these viral inhabitants might help us out.

Young people infected with a type of herpes virus have a better immune response to the flu vaccine than those not infected, scientists at Stanford University report Wednesday. In mice, the virus directly stops influenza itself.

We’re talking about a ubiquitous critter, called cytomegalovirus. About half of all Americans carry it. And so do nearly 100 percent of people in developing countries.

In younger people, CMV had the opposite effect that Davis had predicted: “The virus ramped up the immune system to give better protection from pathogens,” Mark Davis says. “We tested only for the flu, but I speculate it protects against everything.”

So should we all go out and get infected with CMV? No way! Davis exclaims.

You see, CMV has a dark side. It can become dangerous if the immune system is suppressed, which happens after an organ transplant or during treatments for autoimmune disorders. CMV is also a concern for pregnant woman. It’s the top viral cause of birth defects worldwide.

The human microbiome is incredible and teams with thousands of species (bacteria, viruses, members of domain Archaea, yeasts, single-celled eukaryotes, helminth parasites and bacteriophages). The complexity of interactions between all the elements of what is in our bodies and cells is one of the things that makes health care so challenging. It is also fascinating how these interactions provide benefits and costs as they work within our bodies.

The fact that we have evolved in concert with all these interactions is one of the big problems with anti-biotics. Antibiotics are miraculous when they work, but they can also decimate our natural micro-biomes which does create risks.

I would have thought Stanford wasn’t still supporting closed science :-( Sadly this research is not published in an open science manner.

Related: Foreign Cells Outnumber Human Cells in Our BodiesMicrobes Flourish In Healthy PeopleTracking the Ecosystem Within UsPeople Have More Bacterial Cells than Human CellsCats Control Rats With ParasitesSkin Bacteria

Yacouba Sawadogo – The Man Who Stopped the Desert

Quote from the video

Yacouba single-handedly had more impact on the soil conservation in the Sahel than than all the national and international researchers combined.

Dr. Chris Reij, Vrije University of Amsterdam.

As is normally the case making improvements in the real world is challenging and visionaries often face setbacks. Even when they have success that success is threatened by those that want to take the rewards but ignore the lessons. The clip above is a excerpt from the documentary film on his efforts.

Meet Yacouba Sawadogo – The Man Who Stopped the Desert

The simple old farmer’s re-forestation and soil conservation techniques are so effective they’ve helped turn the tide in the fight against the desertification of the harsh lands in northern Burkina Faso.

Over-farming, over-grazing and over population have, over the years, resulted in heavy soil erosion and drying in this landlocked West African nation.

Zai is a very simple and low-cost farming technique. Using a shovel or an axe, small holes are dug into the hard ground and filled with compost. Seeds of trees, millet or sorghum are planted in the compost. The holes catch water during the rainy season, so they are able to retain moisture and nutrients during the dry season.

According to the rules of Zai, Yacouba would prepare the lands in the dry season – exactly the opposite of the local practice. Other farmers and land chiefs laughed at him, but soon realized that he is a genius. In just 20 years, he converted a completely barren area into a thriving 30-acre forest with over 60 species of trees.

Yacouba has chosen not to keep his secrets to himself. Instead, he hosts a workshop at his farm, teaching visitors and bringing people together in a spirit of friendship. “I want the training program to be the starting point for many fruitful exchanges across the region

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2014 Ranking of the World’s Best Research Universities

Shanghai’s Jiao Tong University produces an annual ranking of research universities. The methodology values publications and faculty awards (Nobel and Fields) which belies the focus on ranking research not for example the quality of education provided.

You could argue one measure does partially address teaching as the Nobel and Fields prizes to alumni are created to the institution (that is separate from a measure of faculty that receive those honors). I would agree it partially measure the education though it also measures the ability of that school to attract the absolute best candidates (whether they would have been just as successful going elsewhere is a fair question).

Results from the 2014 rankings of top 500 universities with the number of schools by country:

location Top 100 % of World
Population
% of World GDP % of top 500
USA 52     4.5%   22.2%  29.2%
United Kingdom   8  0.9  3.5 7.6
Germany   4  1.1  5.0 7.8
Canada   4  0.5  2.4 4.2
France   4  0.9  3.8 4.2
Japan   3  1.8  7.8 3.8
Australia   4  0.3  1.5 3.8
China   0  19.2  11.7 8.8
Netherlands   4  0.2  1.3 2.6
Sweden   4  0.1  0.8 2.2
Switzerland   5  0.1  0.8 1.4
South Korea   0  .7  1.7 2.0
India   0  17.0  1.9 0.2

The top countries for top 100 and top 500 schools are listed above, but I skip over many after the top 7 or 8 to include a few countries I like to watch, see the ranking site for the full list. Country population and GDP data were taken from the World Development Indicators 2013, by the World Bank.

There is little change in top 100 since 2008, which I think is a good sign, it wouldn’t make much sense to have radical shifts quickly in this type of ranking. The USA lost 2 schools in the top 100, UK lost 3, Germany lost 2, Switzerland gained 2, Netherlands gain 2…

There is more change in the top 500 where changes are more sensible (there is probably not much separating schools ranked in the 300’s from those in the 500’s so variation and strong pushes (from countries like China) can have an impact. China gained 14 more schools in the top 500. China’s GDP also increased from 6.6% of global GDP to 11.7%.

University of Wisconsin – Madison is 24th, it was 17th in 2008 My father taught there while I grew up.
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Teixobactin – New Antibiotic Attacks Ability of Bacteria to Build Cell Walls

New class of antibiotic could turn the tables in battle against superbugs

The antibiotic, called teixobactin, kills a wide range of drug-resistant bacteria, including MRSA and bugs that cause TB and a host of other life-threatening infections.

It could become a powerful weapon in the battle against antimicrobial resistance, because it kills microbes by blocking their capacity to build their cell walls, making it extremely difficult for bacteria to evolve resistance.

It would be great if the exciting results carried through to real world results similar to the hope. Medical research is full of promising initial results that fail to deliver, however. We are at great risk if some new miracle anti-biotic isn’t found. Many people are investigating potential solutions.

Most antibiotics are isolated from bacteria or fungi that churn out lethal compounds to keep other microbes at bay. But scientists have checked only a tiny fraction of bugs for their ability to produce potential antibiotics because 99% cannot be grown in laboratories.

Lewis’s group found a way around the problem by developing a device called an iChip that cultures bacteria in their natural habitat. The device sandwiches the bugs between two permeable sheets. It is then pushed back into the ground where the microbes grow into colonies.

Working with a Massachusetts-based company, NovoBiotic, and researchers at the University of Bonn, [Kim] Lewis’s group screened 10,000 soil bacteria for antibiotics and discovered 25 new compounds. Of these, teixobactin was the most promising.

Though promising, Lewis said that years more work lie ahead before the drug could be available. Human clinical trials could begin within two years to check its safety and efficacy, but more development would follow that.

It is wonderful to read about the great work so many scientists are making in researching potential life saving drugs. Hopefully this antibiotic will save us from what will be catastrophic harm if some new antibiotic is not available soon.

Related: Search for Antibiotic Solutions Continues: Killing Sleeper Bacteria Cells (2013)New Family of Antibacterial Agents Discovered (2009)Potential Antibiotic Alternative to Treat Infection Without Resistance (2012)

Ranking Countries by Scientific Publication Citations: USA, UK, Germany…

The SCImago Journal and Country Rank provides journal and country scientific indicators developed from the information contained in the Scopus database. I posted about this previously (in 2014, 2011 and 2008).

The data in the post is based on their data from 1996 through 2013. The web site also lets you look at these ranking by very specific categories. For example biotechnology #1 USA, #2 Germany, #3 UK, #4 Japan, #12 China or human computer interaction #1 USA, #2 Germany, #3 UK #4 Japan, #13 China).

I like looking at data and country comparisons but in doing so it is wise to remember this is the results of a calculation that is interesting but hardly definative. We don’t have the ability to measure the true scientific research output by country.

The table shows the top 6 countries by h-index and then some others I chose to list.

Country h-index 2010
h-index
2007
h-index
% of World
Population
% of World GDP total cites
USA 1,518 1,139 793     4.5%   22.2% 152,984,430
United Kingdom 918 689 465  0.9  3.5 37,450,384
Germany 815 607 408  1.1  5.0  30,644,118
France 742 554 376  0.9  3.8  21,193,343
Canada 725 536 370  0.5  2.4 18,826,873
Japan 635 527 372  1.8  7.8 23,633,462
Additional countries of interest (with 2013 country rank)
16) China 436 279 161  19.2  11.7  14,752,062
19) South Korea 375 258 161    .7  1.7  5,770,844
22) Brazil 342 239 148  2.8  3.0 4,164,813
23) India 341 227 146  17.5  2.6 5,666,045

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Manufacture Biological Sensors Using Silk and Looms

The fabric chip platform from Achira Labs in India uses looms to manufacture biological sensors.

Image of process for creating silk test strips

image by Achira Labs

Yarn coated with appropriate biological reagents like antibodies or enzymes is woven into a piece of fabric at the desired location. Strips of fabric are then cut out, packaged and can form the substrate for di erent biological assays. Even a simple handloom could produce thousands of these sensors at very low cost.

The resulting fabrics can be used to test for pregnancy, diabetes, chronic diseases, etc.. Achira Labs, an Indian start-up, received $100,000 in Canadian funding in 2013 to develop a silk strip that can diagnose rotavirus, a common cause of diarrhea and can be used in diapers.

The company is planing to start selling silk diabetes test strips using there process this year and expects costs to be about 1/3 of the existing test strips using conventional manufacturing processes.

Related: Appropriate Technology Health Care Solution Could Save 72,000 Lives a YearWater WheelUsing Drones to Deliver Medical Supplies in Roadless AreasAppropriate Technology: Self Adjusting Glasses

Defying Textbook Science, Study Finds Proteins Built Without DNA Instructions

Open any introductory biology textbook and one of the first things you’ll learn is that our DNA spells out the instructions for making proteins, tiny machines that do much of the work in our body’s cells. Results from a recent study show for the first time that the building blocks of a protein, called amino acids, can be assembled without blueprints – DNA and an intermediate template called messenger RNA (mRNA). A team of researchers has observed a case in which another protein specifies which amino acids are added.

“This surprising discovery reflects how incomplete our understanding of biology is,” says first author Peter Shen, Ph.D., a postdoctoral fellow in biochemistry at the University of Utah. “Nature is capable of more than we realize.”

To put the new finding into perspective, it might help to think of the cell as a well-run factory. Ribosomes are machines on a protein assembly line, linking together amino acids in an order specified by the genetic code. When something goes wrong, the ribosome can stall, and a quality control crew is summoned to the site. To clean up the mess, the ribosome is disassembled, the blueprint is discarded, and the partly made protein is recycled.

Yet this study reveals a surprising role for one member of the quality control team, a protein conserved from yeast to man named Rqc2. Before the incomplete protein is recycled, Rqc2 prompts the ribosomes to add just two amino acids (of a total of 20) – alanine and threonine – over and over, and in any order. Think of an auto assembly line that keeps going despite having lost its instructions. It picks up what it can and slaps it on.

“In this case, we have a protein playing a role similar to that filled by mRNA,” says Adam Frost, M.D., Ph.D., assistant professor at University of California, San Francisco (UCSF) and adjunct professor of biochemistry at the University of Utah. He shares senior authorship with Jonathan Weissman, Ph.D., a Howard Hughes Medical Institute investigator at UCSF, and Onn Brandman, Ph.D., at Stanford University. “I love this story because it blurs the lines of what we thought proteins could do.”

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Virgin Births in the Animal Kingdom

Spectacular and Real Virgin Births

Scientists are discovering that virgin births occur in many different species; amphibians, reptiles, cartilaginous and bony fish and birds and it happens for reasons we don’t quite understand.

Initially, a virgin birth, also known as parthenogenesis, was thought to be triggered by extreme situations; it was only documented among captive animals, for example, perhaps by the stress, or isolation. A way to continue the bloodline when all other options had gone, when there was no other choice.

Not necessarily. It now appears that some virgin females produce offspring even in the presence of males.

Another interesting area of research for scientists. The value of sex to aid a species’ success is well understood. The value of being able to produce offspring when no males are around seems obvious also. But how this all works is quite interesting and again shows how much we have to learn.

Related: Fungus-gardening Ant Species Has Given Up Sex Completely (2010)Some Female Sharks Can Reproduce All by Themselves (2007)Amazon Molly Fish are All Female (2008)Bdelloid Rotifers Abandoned Sex 100 Million Years Ago (2007)

Leslie Lamport Receives 2013 ACM Turing Award

Leslie Lamport, a Principal Researcher at Microsoft Research, has been named as the recipient of the 2013 ACM A.M. Turing Award for imposing clear, well-defined coherence on the seemingly chaotic behavior of distributed computing systems, in which several autonomous computers communicate with each other by passing messages. He devised important algorithms and developed formal modeling and verification protocols that improve the quality of real distributed systems. These contributions have resulted in improved correctness, performance, and reliability of computer systems.

ACM (Association for Computing Machinery) announced that the funding level for the ACM Turing Award is now $1,000,000 (to be provided by Google). The new amount is four times its previous level. It seems to me the 14th of November 2014 is a bit late to announce the 2013 award winner, but for an extra $750,000 I would gladly wait a year (or a decade for that matter).

The new award level brings the computer science award to the level of Nobel Prizes and the Fields medal.

Leslie Lamport’s 1978 paper, “Time, Clocks, and the Ordering of Events in a Distributed System,” one of the most cited in the history of computer science.

Read more about the work of Leslie Lamport.

Related: Barbara Liskov wins Turing Award (2009)Donald Knuth, Computer Scientist (2006)Google 2006 Anita Borg Scholarship2008 Draper Prize for Engineering

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